Applied Microbiology and Biotechnology

, Volume 102, Issue 15, pp 6613–6625 | Cite as

Comparative transcription profiling of two fermentation cultures of Xanthomonas campestris pv. campestris B100 sampled in the growth and in the stationary phase

  • Rabeaa S. AlkhateebEmail author
  • Frank-Jörg Vorhölter
  • Tim Steffens
  • Christian Rückert
  • Vera Ortseifen
  • Gerd Hublik
  • Karsten Niehaus
  • Alfred Pühler
Genomics, transcriptomics, proteomics


The ɣ-proteobacterium Xanthomonas campestris pv. campestris (Xcc) is the producer of the biopolymer xanthan, a polysaccharide which is used as a thickener in numerous industrial applications. In this study, we present a global transcriptome profiling of two Xcc strain B100 cultures obtained from fermentation during the growth phase and the subsequent stationary phase associated with xanthan biosynthesis. During the xanthan production phase, highly abundant transcripts belonged to genes encoding for small RNAs, glycogen biosynthesis, and xanthan export. A total of 1850 (40%) genes were differentially transcribed during the stationary phase where 924 were transcriptionally up-regulated and 926 genes were down-regulated. An overview of differentially transcribed genes includes a significant down-regulation of genes involved in transcription, translation, and amino acid biosynthesis pathways. A group of up-regulated genes was involved in cellular response against oxidative stress, such as those coding for superoxide dismutase and catalase. Genes encoding enzymes involved in nucleotide sugar precursor synthesis of xanthan biosynthesis, such as xanA, galU, and ugd, exhibited a transcription pattern that did not change during the growth and stationary phase. Regarding the transcription pattern of the gum gene cluster that govern xanthan biosynthesis, a significant up-regulation of the genes gumB, gumC, and gumD was observed, while the transcript pools of the genes gumG, gumH, gumI, and gumJ were reduced and those of genes gumE, gumF, gumK, gumL, and gumM remained un-changed during the stationary phase compared to the growth phase. The obtained data represents the first analysis of gene expression patterns under xanthan production conditions and provides the bases for future studies aiming at enhancing xanthan yield.


Xanthan biosynthesis RNA sequencing Differential transcriptomics Xanthomonas Plant pathogen 



R.S. Alkhateeb and T. Steffens acknowledge the support from the CLIB Graduate Cluster Industrial Biotechnology at Bielefeld University as associate fellows. The bioinformatics support of the BMBF-funded project Bielefeld-Gießen Center for Microbial Bioinformatics—BiGi within the German Network for Bioinformatics Infrastructure (de.NBI) is gratefully acknowledged.

Funding information

This study was funded by a Ph.D. grant received from Jungbunzlauer AG, Austria to the CLIB Graduate Cluster Industrial Biotechnology.

The authors would like to thank our co-operation partners from Jungbunzlauer AG, Austria, for granting the financial support to this project.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

This article does not contain any studies with human participants or animals performed by any of the authors.

Supplementary material

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Center for Biotechnology (CeBiTec)Bielefeld UniversityBielefeldGermany
  2. 2.Department of Proteomics and Metabolomics, Faculty of BiologyBielefeld UniversityBielefeldGermany
  3. 3.MVZ Dr. Eberhard & Partner DortmundDortmundGermany
  4. 4.Xell AGBielefeldGermany
  5. 5.Technology Platform Genomics, Center for Biotechnology (CeBiTec)Bielefeld UniversityBielefeldGermany
  6. 6.Jungbunzlauer Austria AGWulzeshofenAustria

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